Abstract
Squamate pregnancy is an important topic in reproductive and evolutionary biology, as it provides insight to amniote live‐bearing that is not mammalian. Gene regulation in squamates is poorly characterised and the extent of molecular convergence in the developmental mechanisms of pregnancy across amniotes is strongly debated. To test the role of gene expression and alternative splicing in viviparous pregnancy in a lizard, we sequenced the uterine transcriptome of viviparous female Eurasian common lizards (Lacertidae: Zootoca vivipara ) using long reads and examined whole‐gene and transcript‐level expression before, during, and after pregnancy. We found that 874 genes were differentially expressed between pregnant and non‐pregnant uterine tissue, including several involved in pregnancy in other animals, such as NOS1, MALL, and CLCN2. Upregulated genes were enriched for functional terms relevant to pregnancy in other amniotes, such as cardiovascular, tissue remodelling, and muscle‐related processes; downregulated terms were dominated by ribosomal activity. We found differential transcript usage between reproductive stages for 114 genes, of which most (78 genes) were not differentially expressed, suggesting alternative splicing and expression play different functional roles. Genes showing differential transcript usage included several with isoform variants involved in pregnancy in mammals and/or squamates, such as SRSF2, FAU, and LPP. These candidates involved alternative promoters and complex patterns of regulation varying by isoform across reproductive stages. Our study provides high‐resolution information about gene regulation during viviparous lizard reproduction, indicating a functional role of differential expression and alternative splicing involving new candidates and others known to be involved in amniote pregnancy.